While You Were Gone
by HolbyCityFan13
Summary: 2 weeks after Sherlock's death, Molly is lonely. She isn't sure if the theories are right, if he managed to survive the fall somehow, or if she should try to move on, but she soon discovers something which makes her wish for him to come back, because the only time she truly needs him, he's gone. Eventual Sherlolly and John/Mary.
1. 1 Theories

Molly's phone pinged. 1 new email. She sighed as she picked it up to read the email. It was probably someone wanting an interview about Sherlock - she'd been asked to do 4 last week, and in the end the only thing she'd agreed to was a witness statement for the police enquiry. So far they'd concluded that it was probably suicide, though someone had managed to misplace the body, so they couldn't be sure. How could anyone lose a body? It wasn't exactly hard to take it down to the morgue.

She unlocked her phone and selected read email.

T_o; mhooper _

_From; philanderson .uk_

_Molly,_

_So far there are four possibilities of what could have happened on the rooftop. In most of these scenarios, Sherlock had a team of people who were aware of these possibilities, with specific code words given for each outcome..._

Molly stopped reading at that. Anderson could come up with all the theories he liked - none of them would bring Sherlock back. Even if he had survived, there would have been a reason he'd faked his death, so coming back to Baker Street two weeks later probably wouldn't be a possibility. The lack of body hinted at his survival, but there was no solid evidence, and they needed solid evidence to be sure. All the theories started with What if or Maybe.

She skimmed the rest of Anderson's theories and frowned. All of them required a team of people knowing about Sherlock's plans, something that seemed like a very un-Sherlock thing to do. Maybe that was why he did it. But if he was alive, he would have left something - some sort of message, just something to let her - and probably John - know that he wasn't dead. Something more than a lack of a corpse. Molly glanced at the clock and sighed. 11:48. She could think about it again in the morning.

**A/N: Sorry it's short, the rest of the chapters will be longer! Please let me know what you think so far!**


	2. 2 Finding out

Molly sat on the edge of the bath, impatiently fiddling with the white stick in her hands. She had noticed this morning that she hadn't started her period yet - it was nearly a week late, but since Sherlock died, she'd forgotten about everything else. She'd worked nearly every day for the last 2 weeks, because it helped - it made her think about something other than whether he was alive or not - and everything else had faded into the background. Molly hadn't seen John since the day that it happened, when he'd bumped into her on the stairs, to tell her what happened. He didn't know that she'd seen it too - she was on the other side of the lab, but she saw Sherlock falling past the window. She'd rushed to the window and seen him lying on the pavement. Blood was pouring from a cut on his face. She'd seen John push past the group of doctors and nurses surrounding the body, only to be held back as they lifted him onto a stretcher. She'd watched every minute of it from the window.

Molly thought back to 3 weeks before Sherlock 'd been at the pub, and in a few hours both of them were drunk. Sherlock had invited her back to 221b, Baker Street. One thing had led to another, and eventually they'd ended up sleeping together. Her gaze fell to her watch, stating that 3 minutes had passed since she'd taken the test, then back to the object in her hands. It lay face down across her palm, and it took Molly 20 seconds to work up the courage to turn it over.

It was paler than the first, but the second line was definitely there. It wasn't one of those I-can't-tell-I'll-do-another-test results. It was more of a you-can't-miss-it result. She hadn't planned on having a baby. She hadn't planned having children at all - she had always thought of it as something she would do in the future, if she found the right person. She _definitely_ didn't think Sherlock was the right person. It wasn't that she didn't like him - she'd just never imagined having a child with him. She couldn't imagine what he would do if he was left with a baby. He certainly hadn't wanted a child, but she wasn't so sure about herself. She had never really thought about it until now. She had to make a decision - she had a while to make it, but she'd rather decide sooner than later. Later, she'd panic and end up doing something she regretted.

If it was anyone else, Molly would have known right away, but this was Sherlock. She didn't even know if he was dead or alive. Either way, she'd probably end up doing it on her own, or some of it anyway. Even if he was alive, and he did want the baby, it would probably be months, maybe years before Sherlock could come back . He wouldn't pull a stunt like that for nothing - it would have to be a pretty big problem, and that would take more than faking his death to sort out. He might not even want the baby. He might just be dead - no faking, no clever plans to get out of whatever Moriarty had set up, the lack of body explained by a newbie who had managed to get lost on their way to the morgue, or a scientist forgetting to log which body they used for an experiment. She had to stop thinking about what Sherlock wanted. If he survived, he wouldn't come back for a while anyway, so it was really about what she wanted.

Molly didn't know what she wanted. If she got an abortion, that would be it. Her life could go back to normal - well, as normal as it had been since Sherlock died. If she kept the baby, it would change everything. She'd need to buy tons of things for the baby, redecorate the spare room, sort out maternity leave... There would be so much to do, but she couldn't bear to think about aborting it. She knew exactly what would happen to the baby if she did, and she didn't like thinking about that. The final reason, perhaps that made her decide what she did, was Sherlock. If he really was dead, this baby would be the only part of him she had left.

She'd made up her mind.

**A/N: Thanks for reading! It would be great if you could review and let me know what you think! Next chapter should be up this weekend.**


	3. 3 John

**A/N: I do not own Sherlock. Forgot to mention that last time. Sorry if you find these annoying but it's better to have a few sentences before the chapter than a whole chapter that's just one long sorry about the length of this chapter but next one will be longer, I promise.**

"Do you want a cup of tea, dear?" Mrs Hudson asked. John shook his head and Mrs Hudson disappeared downstairs. John didn't even want to be there - there were too many memories at Baker Street. He'd moved out the day after Sherlock died. He was only there now because Molly had called and asked to meet him somewhere, and Baker Street was the first place he could think of.

Molly paused on the pavement below 221b, Baker wasn't sure if she wanted to tell John, but he would find out sooner or later anyway, and she'd prefer him to hear it from her first. She wasn't sure how he was going to take the news, though she hoped he could be happy for her, at least, no matter how he felt about it being Sherlock's baby. Actually, she realised, John would probably be angry at some point - not at her, she hoped, but at Sherlock. Especially if he came back in a few years time, having survived the fall, just reappearing into their lives as quickly as he'd disappeared. Honestly, she wouldn't put it past Sherlock to do something like that.

It was Mrs Hudson who opened the door.  
"Molly, come in, dear. John's just upstairs." He'd already told Mrs Hudson why he was here, and to stay out of the way as much as she could. "Would you like a cup of tea?" She offered politely.

Molly shook her head as she started walking up the stairs. She'd been surprised when John suggested they meet at 221b, Baker Street. She didn't think he was still living there, but Mrs Hudson hadn't said it was available either. She opened the door to see John sitting on the sofa. He didn't look pleased to be there, but it had only been 3 weeks - and one week since Molly had found out. She almost hadn't come, but John needed to know - Sherlock had been his best friend, after all.

John glanced up at Molly as she opened the door. He was sure she seemed paler than the last time he'd seen her, and definitely more nervous. He guessed it was just a cold, or maybe the flu.

"John," She broke the silence as she sat down opposite him. He looked across at her and smiled weakly. "Molly. How are you?" He asked and she nodded. "I'm okay. Actually, that's kind of why I came." Confusion flickered across John's face. Molly took a deep breath. "I'm pregnant."  
"Congratulations." She sighed.  
"It's...the 's Sherlock's."


	4. 4 The Scan and The Letter

Molly checked her phone for the third time since she'd entered the waiting room.

_2 new emails_

_Read Now| Later_

She pressed_ Read Now. _

_• Google Play:Get the latest apps,games,and books for your smartphone..._ She skipped that one.

_•From _ _Subject: New theory_

She sighed, locking her phone as she slipped it back into her pocket. She still had five minutes before her appointment was due to start. She looked around the waiting room for something to do, but all she could see were a few posters - about "Breast is best" and "Baby's Health" - some similar leaflets, and other women sitting across the room. The first she saw was probably here for her 20 week check up, Molly thought. The one sitting next to her was much younger, probably a teenager, and wasn't visibly pregnant. She thought back to when she'd decided not to have an abortion, and empathised with the teenager - it wasn't an easy decision to make, and Molly hadn't even chosen to have an abortion. She could only imagine how hard that would be. Molly's gaze slid to the door as a young woman slipped out quietly. She clearly didn't want to be seen, and most of the people waiting were distracted anyway. Traces of eyeliner lingered beneath her eyes, even though she'd tried to wipe them off, and Molly quickly came to the conclusion that the young woman had been crying, and the reason why.

'Deducing, concluding...like Sherlock would.' She thought, and immediately regretted it. She felt tears building up in her eyes, but she blinked them back. She couldn't burst into tears in the middle of the busy waiting room. Instead, Molly thought about last week, and telling John. He hadn't been angry, as she'd almost expected him to be - instead, he'd left Baker Street,clearly upset, and called her later to apologise, telling her to call him if she needed anything. "Molly Hooper." The receptionist called as she came out from behind the desk. Molly stood up and followed her down the corridor, then through a door to the right. "Doctor Herden, this is Molly Hooper, your eleven o'clock." The receptionist introduced her before returning the desk. The doctor asked Molly a few questions and flicked through her file before measuring her weight and height. "Now just lie down, and I can do the ultrasound. Roll your top up and I'll get started." The doctor instructed, and Molly obeyed. She lay still as the doctor warned her about the gel - "Now,this might be a little bit cold." - and started moving the wand around. "Do you know how far along you are?" She asked, and Molly nodded. "About 7 weeks." The doctor finally found the baby, and agreed with Molly. "It's a little too early to hear the heartbeat, but baby looks healthy. Would you like any ultrasound pictures printed?" Molly nodded. "Two." The doctor arranged the dates for the twelve and twenty week scans and talked about the possibility of using prenatal vitamins before handing her the pictures. Molly left just as the receptionist appeared in the corridor, showing a heavily pregnant woman into another room.

* * *

**This was originally 2 chapters but they were quite short so I put them together.**

* * *

When Molly got home, she found a letter. Her heart raced at the sight of Sherlock's handwriting on the pale blue envelope. Picking up the envelope, she headed through to the living room, and left her bags by the coffee table. She sat on the sofa and turned over the envelope. She ripped it open and pulled out a letter - and a small parcel. She left the parcel on the table and unfolded the sheet of paper.

_Dear Molly,_

_I'm sorry. It may come as a shock, though the lack of a body was surely a clue, that I am not dead. You can't tell John - he would get involved, try to find me, and that can't happen. No one else can know that I'm alive, not now at least. When I come back, they'll find out, but now is not the time. _

_I'm sorry about that too. I can't come back for a year, until next January. I will keep writing to you, but don't try to write back - I'm undercover and I don't have a permanent address at the moment. I'll keep you up to date though._

_One last thing - that night, 3 weeks before I left - you know which one I mean. I meant it._ _I love you, Molly Hooper - and I'm sorry it has to be like this._ _Enjoy the present._ _Sherlock_

A few words blurred as Molly's tears hit the paper. It was typical of Sherlock, telling her he loved her through a letter, when he wouldn't see her for a year. But she couldn't write back to him, she couldn't talk to him... He wouldn't even know about the baby, who'd be here before he was. She'd tried calling him before, but he obviously didn't have his mobile anymore. She normally have given up there, just wishing she could talk to him, but now it was important. He was alive, and he had to know about the baby. _Mycroft_. That was how she could contact him. Mycroft would know about his plans, in case something went wrong. She dialled his number on her phone and waited as the phone rang.

"I need to talk to Sherlock."

_"Not possible, I'm afraid. My dear brother is-"_

"Mycroft, please. I just got his letter, and it's important."

_"Of course. If you just wait a few seconds, I'll redirect the call..." _Molly heard a few clicks before the line went silent. A few minutes later, it started ringing.

_"Mycroft, if you do that one more time-"_

"Sherlock, it's Molly."

_"Oh. I take it you got the letter?"_

"Yes, but I-"

_"And the present?"_

"Well, yes, but-"

_"No, I can't come back any time before January, and yes, I really need to go now."_

"That's not what I-" He hung up. Mycroft apologised for the shortness of the phone call before Molly hung up. A single tear slid down her cheek. She couldn't help it - Sherlock still didn't know, and Mycroft said he would be starting his undercover work in the next few days. He'd drop all contact with everyone, even his brother. And there would be no way to contact him again until he came back. He wouldn't know until he came back next January, when the baby would be about four months old.

Molly remembered the parcel and picked it up from the coffee table. It was small, wrapped in purple tissue paper. She rolled it across the palm of her hand before she opened it. Inside, there was a ring. Silver, with a metal eye engraved on the outside. A message was engraved inside the wring. _Always here, far or near._ It was beautiful, but it only made Molly cry harder. _Far or near. _That was true enough.

**Thanks for reading! Sorry if the letter from Sherlock was a bit OOC.**


	5. 5 March and April

Molly grabbed the spare ultrasound picture from the table, along with a pen and an envelope. Sherlock had told her not to bother trying to contact him, but she was desperate. He had to know before he came back next year.  
Molly made a note on the back of the picture.  
_Baby Hooper-Holmes (7 week ultrasound)  
I tried to tell you.  
I'm sorry, Sherlock.  
From Molly_  
She slid the ultrasound picture inside the envelope. Her own copy was in the drawer of her desk, waiting to be put in a photo album when she knew the baby's gender. She had already decided that she'd buy a pink one if it was a girl, and blue if it was a boy.  
She closed the envelope and flipped it over, writing Sherlock on the front. As an afterthought, she added a note on the back for Mycroft.  
_Mycroft, please get this to Sherlock as soon as you can. I know he can't come back, not yet anyway, but he should know.  
Molly._  
She pulled on her coat and dropped the envelope into her pocket. It was raining, but the cemetery wasn't far.

Molly was surprised when she saw the amount of flowers and messages left at his grave. But he did save a lot of people from going to jail, and worse. She slipped the envelope under some clear plastic someone had covered the flowers with, right at the front, in the hope that Mycroft would find it, and possibly pass it on to his brother.

She got home to find another letter from Sherlock, just mentioning how he hoped John wasn't dealing with it too badly and that she was okay. She wished she could tell him, but even Mycroft probably didn't know where he was.

~•~•~•~•~•~•~  
**1 week later**  
"So you had your last ultrasound at 7 weeks, correct?" The doctor checked as she glanced at Molly's file. Molly nodded.  
"This ultrasound will be very similar to your last one, but as you are twelve weeks now, we should be able to listen to the heartbeat as well."  
Molly rolled her top up and the doctor placed the wand on the slight curve of her abdomen, moving it around a little to get a clearer image. A pale shape flickered onto the screen. It was more detailed than the last time Molly had seen it, and now she could make out the shape of its face and hands. She wished Sherlock was here with gaze drifted from the screen to the ring he had sent her, as it often did when she thought of him. She'd thought, at first, that it might conceal a tiny camera or microphone - it was the sort of thing he might do - but an X-ray revealed it was simply a silver ring.  
"Would you like to hear the baby's heartbeat?" The doctor interrupted Molly's thoughts. Molly nodded. The doctor pressed a few buttons and a steady beat filled the room. A few seconds later, she switched it off again, and after taking some of the baby's measurements, she moved on to the topic of ultrasound pictures.  
"How many would you like printed?" Molly hesitated. She found herself wishing, again, that Sherlock was here with her.  
"Two." She had decided that, after last week, she would leave the ultrasounds and baby photos by Sherlock's grave, and hopefully  
Mycroft would pick them up and be able to get them to his brother.

* * *

**A/N: This was 2 chapters, but they were** **pretty short so I put them together.**

* * *

**1 month later **

The letter dropped onto the carpet quietly. It was the noise of the letterbox opening and closing that brought Molly to the door. She crouched down to pick it up, resting a hand on top of her growing bump as she regained her balance. She glanced at the neat handwriting as she stood up and headed into the living room. She had come to expect these letters now - they usually arrived towards the end of the month, usually asking how she was, as if she could write back, and how John was, and how he hoped there had been some interesting cases on the news recently. Molly sat on the sofa and ripped open the top of the envelope. She unfolded the letter to find that it looked longer than usual, the page filled with loops of black ink.

_Dear Molly,_

_I hope you and John are okay. Mycroft called yesterday, said he had something to tell me, but I doubt that it was of any significance - it was probably just . case that he wanted me to come back and solve. I was forced to hang up before he told me - any more calls from that phone and they'd find me in minutes, so I chucked it in the river. That's one problem solved. The other problem is the letters. I can't keep writing to you, not every month, or they'll trace them back to me. I'm sorry.I'll write when I can. Don't write back._

_Sherlock._

**A/N: Again, sorry if Sherlock seems OOC. **


	6. 6 May and June

**1 month later**

Molly sighed as she sat down on the sofa. She glanced at her watch and noticed she only had half an hour before she had to be at the hospital for her 20 week scan.

She felt the baby move inside her womb as she rested her hand on the top of her growing bump. She had been feeling her son or daughter's movements for a few weeks now,but she was still waiting to feel him or her kick.

Molly grabbed her handbag and left the flat, getting a cab to the hospital. She got there with 10 minutes to spare before her appointment, and took one of the few empty seats in the waiting room. Glancing around the busy room, she noticed several mothers, some cradling young babies, and toddlers or children clutching the hands of others. Molly began to wonder what her own child would look like. She'd have a better idea later that day, when she'd found out the gender of the baby, but for now, she could imagine. For some parts the gender didn't matter - either way, their little boy or girl would definitely have Sherlock's curly hair - that was one thing she knew for certain. He or she would probably have his piercing eyes too - she could even imagine the child being identical to him, complete with a long black coat and scarf over a smart suit. But the logical part of her knew that it was highly unlikely - the child would inherit some qualities from her too. Maybe they would have curly brown hair, the same shade as her own, or perhaps their eyes would be-

Molly's thoughts were interrupted by a shout from the desk. "Molly Hooper, please." The receptionist said, barely looking up from the computer screen. Molly stood up and made her way through the crowded room - she was sure it had been quieter ten minutes ago - towards the desk.

"First room on the right, it's Doctor Herden." The receptionist told her as she typed something up on the computer. She nodded and followed the instructions to the right room.

After the doctor took her height and weight, Molly was instructed to lie back as the doctor prepared the scanner. She warned Molly about the gel being cold and started moving the scanner over her bump.

"Would you like to know the gender?" The doctor asked and Molly nodded, her eyes still fixed on the black and white image on the screen.

"You're having a girl." The doctor told her, and she smiled. She could imagine her daughter already - a little girl running through the park, brown curls bouncing around her shoulders as she turned around. Her piercing blue eyes and curly hair were identical to Sherlock's, but everything else was Molly's. Her hair, apart from the curls, her features, apart from the eyes...

She was snapped out of her imagination by the doctor, asking how many scan pictures she wanted printed - the answer was two, as always - and telling her that she could go. Molly picked up the pictures and left, stopping at her flat to get some paper and a pen before she went to Sherlock's grave.

_Baby Hooper-Holmes_

_20 weeks_

_It's a girl :) _

_From Molly_

She wrote on the back of the scan picture. She pulled the paper out of her bag and wrote a quick note before she slid both of them into an envelope, writing Sherlock on the front, flipping it over and writing via Mycroft on the back. She placed it in front of the new bunches of flowers and cards.

* * *

**A/N: Before you read this part, I just wanted to mention that in this fanfic, (1) Molly and Mary have been friends for a few years. (2) That is how Mary met John. (3) Mary and John started dating a few months before Sherlock 'died', but Sherlock wrongly assumed it would only last a few more weeks, and they are still together. And sorry this chapter is so short and sorry for all the time skips, there will be less after the baby's born.**

**The next chapter should be up soon as the first part/short chapter is already written.**

**1st June 2013**

Mary smiled as she picked up another pink onesie. After she'd found out that Molly was having a girl, she'd dragged her on a shopping trip. They were only going to buy clothes, but then Molly had mentioned that she still needed to sort the baby's room, and Mary had decided to help with everything, though it would take a few weeks, at least.

She turned around and showed Molly the clothes she'd chosen. Molly shook her head.

"Why not? They're cute!" Mary protested.

"They're too... girly." She sighed at Molly's response.

"Because they're _for_ a girl."

"That doesn't mean everything has to be pink!"

Mary gave up and put the clothes back. She turned to ask Molly something, but paused when she saw her friend gasp and her hand fly to her bump. She was by her side in seconds.

"What's wrong? Is it the baby?" Mary asked.

A small smile formed on Molly's lips.

"She's kicking."

**4pm**

"That's the baby's room painted." Mary said triumphantly as she put the paintbrush down.

"I've still got to put up all the furniture." Molly reminded her.

"We'll do that tomorrow." Mary promised. She looked around the room and smiled. All four walls were painted a pale lilac. Most of the furniture wasn't painted, but Molly had bought pink and purple blankets and clothes.

Mary knew that most people probably didn't have everything ready this early, with 19 weeks left until Molly's due date, but she also knew that Molly wouldn't want to be sorting out furniture and clothes last minute.

Anyway, they hadn't sorted _everything_ yet. They still had to put up the furniture in the baby's room, and buy a car seat and a pram, though they could do most of that tomorrow. And Molly still needed to buy nappies, and probably some more clothes, and bottles, and there was probably something else she'd forgotten, but she had 19 weeks to do that.


	7. e Last Letter

**A/N: Sorry for the time skip but I had no idea what could happen between the events of the last chapter and this one, so here it sorry it's short and really boring. It's just a really really short filler.**

** I also wanted to say thank you to kat4384 for the review because a lot if people just say "update soon" and don't really appreciate how much work goes into writing these and how nice it is to get reviews that are more than a few words.**

**Sorry about how short this chapter is but it didn't fit with the last or the next chapter so I had to put it on its own.**

15th July 2013

Molly hadn't expected another letter. When Sherlock had said he'd write when he could, she didn't think he'd actually write again, which is why she was surprised when, one hot day in the middle of July, another letter from him dropped onto the carpet by the door.

She picked it up and took it into the living room to open.

_Dear Molly,_

_This will probably be the last letter that I will write to you before I come back. I might be back before January, November at the earliest. I have destroyed at least half of Moriarty's secret network - it depends how long it takes to destroy the rest. _

_I'll be back soon. Just a few months._

_I love you._

_From Sherlock._

As Molly folded the letter up and put it in the top drawer of her bedside table, she felt her daughter start kicking again, as if she was didn't want her to put it away. Molly paused, placing her left hand on top of her bump.

"I know, baby. Daddy will be here soon." She whispered.


End file.
